Fix delly

Clinical-Genomics · Jul 29, 2021 · b6631aa · b6631aa
1 parent 060cec3
commit b6631aa
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule b/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule
@@ -55,7 +55,8 @@ rule delly_tumor_only:
         bamT = bam_dir + tumor_bam,
         excl = config["reference"]["delly_exclusion_converted"],
     output:
-        final = vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".delly.vcf.gz"
+        final = vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".delly.vcf.gz",
+        namemap= vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".delly.sample_name_map",
     benchmark:
         benchmark_dir + 'delly_tumor_only_' + config["analysis"]["case_id"] + "_delly.tsv"
     singularity:

diff --git a/BALSAMIC/utils/models.py b/BALSAMIC/utils/models.py
@@ -162,7 +162,7 @@ class VCFModel(BaseModel):
     manta_germline: VarcallerAttribute
     haplotypecaller: VarcallerAttribute
     TNscope_umi: VarcallerAttribute
-    delly: VarcallerAttribute
+#    delly: VarcallerAttribute
 
 class AnalysisModel(BaseModel):
     """Pydantic model containing workflow variables